How can I explore tSNE/UMAP plots?

One of the goals of exploring a tSNE/UMAP map (as with any other dimensionality-reduced datasets) is to characterize the populations defined by it. In cytometry, this means defining the phenotypes of populations/”islands” defined on the plots to give them biologically-relevant naming. FCS Express allows users to efficiently explore and name populations in multiple ways: classical backgating, parameter overlays and density plots.

One of the most important steps in high-dimensional data analysis is the exploration of the dimensionality-reduced dataset obtained after tSNE, UMAP or other dimensionality-reduction algorithms. One of the aims of this step is the biological classification of the different populations mapped on the map. In FCS Express this process is extremely easy and dynamic.

Some options and ideas for visualization and analysis are presented below.

After creating a gate around population of interest on the dimensionality-reduced dataset (e.g. tSNE map, UMAP map, PCA, map,...) the population of interest can be backgated on classical 2D Color Dot Plots.

The gate of interest can then be moved around on the map allowing you to immediately see the population of interest backgated on Color Dot plots which will update in real time.

Tip 1: the NxN Multiplots feature can be used to quickly create an NxN matrix of plots.

Tip 2: the population of interest can be emphasized to make its identification easier on Color Dot Plots which is especially useful when the population is rare.

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